The Norway star was left out of the squad for Wednesday's Champions League clash with Lazio at Signal Iduna Park.
Dortmund tweeted to confirm the 20-year-old has a muscle problem, which he reportedly sustained in training.
The news is a blow for Lucien Favre's side, who will secure qualification for the last 16 by avoiding defeat to Lazio.
Erling Haaland (hamstring injury) and Emre Can (muscular problems) are not available in today’s squad.— Borussia Dortmund (@BlackYellow) December 2, 2020
Get well soon, boys! 🙏
Haaland has scored 16 goals in the competition at a rate of one every 56 minutes, which is the best average of any player with at least 10 goals in the competition. He is just three short of Ole Gunnar Solskjaer's record of 19 for a Norwegian player.
Former Salzburg striker Haaland also has 10 goals in eight Bundesliga appearances in 2020-21 for a Dortmund side who sit four points behind leaders Bayern Munich after nine games.
They face Eintracht Frankfurt on Saturday before next Tuesday's final Champions League group game against Zenit.